2-207492268-C-T

Position:

• chr2-207492268-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412387.5(ENSG00000223725):​n.260+25352G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 146,286 control chromosomes in the GnomAD database, including 14,183 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (14183 hom., cov: 29)
• Consequence: ENST00000412387.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000412387.5	n.260+25352G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000418850.1	n.256+25352G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.384 AC: 56114 AN: 146170 Hom.: 14159 Cov.: 29

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.348

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.384 AC: 56189 AN: 146286 Hom.: 14183 Cov.: 29 AF XY: 0.388 AC XY: 27637 AN XY: 71306

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.356

Alfa AF: 0.330 Hom.: 5604

Asia WGS AF: 0.372 AC: 1293 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6755425; hg19: chr2-208356992;